Finished teca_2d_component_area

.gitignore

@@ -1,4 +1,6 @@
 *.sw[a-z]
 *.patch
 _build
+xml
 *.pt
+.DS_store

alg/teca_2d_component_area.h

@@ -12,38 +12,38 @@ TECA_SHARED_OBJECT_FORWARD_DECL(teca_2d_component_area)
 
 /// an algorithm that computes the area of labeled regions
 /**
-Given a set of labels on a Cartesian mesh, the algorithm computes the area of
-each region. Regions are identified by assigning a unique integer value to each
-mesh point that belongs in the region. The component_variable property names
-the variable containing the region labels.
-
-if the region labels start at 0 and are contiguous then an optimization can be
-used. Set contiguous_component_ids property to enable the optimization. Note that
-TECA's connected component labeler assigns the background (i.e. cells not inside
-the segmentation) the label 0. One can identify the background region and area
-via this label. When processing data generated outside of TECA it might be
-necessary to supply the background label. Use -2 if there is no background.
-
-the input dataset is passed through and the results of the calculations are
-stored in the output dataset metadata in the following keys:
-
-    number_of_components - number of component ids for which area was
-                           computed. Note that this can include a background
-                           component i.e. for cells outside of the segmentation.
-
-    component_ids - a vector containing the label of each component. This is
-                    always starts with 0, where the label 0 identifies cells
-                    out side of the segmentation, and ranges up to
-                    number_of_components - 1, where the labels from 1 up to
-                    number_of_components - 1 identify connected regions of
-                    cells inside the segmentation.
-
-    component_area - a vector containing the area for the corresponding entry
-                     in the component_ids array.
-
-    background_id - the label used for cells outside of the segmentation,
-                    i.e. the background. This can be used to skip processing
-                    of the background when desirable.
+  Given a set of labels on a Cartesian mesh, the algorithm computes the area of
+  each region. Regions are identified by assigning a unique integer value to each
+  mesh point that belongs in the region. The component_variable property names
+  the variable containing the region labels.
+
+  if the region labels start at 0 and are contiguous then an optimization can be
+  used. Set contiguous_component_ids property to enable the optimization. Note that
+  TECA's connected component labeler assigns the background (i.e. cells not inside
+  the segmentation) the label 0. One can identify the background region and area
+  via this label. When processing data generated outside of TECA it might be
+  necessary to supply the background label. Use -2 if there is no background.
+
+  the input dataset is passed through and the results of the calculations are
+  stored in the output dataset metadata in the following keys:
+
+      number_of_components - number of component ids for which area was
+                             computed. Note that this can include a background
+                             component i.e. for cells outside of the segmentation.
+
+      component_ids - a vector containing the label of each component. This is
+                      always starts with 0, where the label 0 identifies cells
+                      out side of the segmentation, and ranges up to
+                      number_of_components - 1, where the labels from 1 up to
+                      number_of_components - 1 identify connected regions of
+                      cells inside the segmentation.
+
+      component_area - a vector containing the area for the corresponding entry
+                       in the component_ids array.
+
+      background_id - the label used for cells outside of the segmentation,
+                      i.e. the background. This can be used to skip processing
+                      of the background when desirable.
 */
 class teca_2d_component_area : public teca_algorithm
 {
@@ -58,17 +58,41 @@ class teca_2d_component_area : public teca_algorithm
     TECA_SET_ALGORITHM_PROPERTIES()
 
     // set the name of the input array
+    /*! \fn set_component_variable(const std::string &v)
+
+       set the name of the input array.
+    */
+    /*! \fn get_component_variable() const
+
+       get the name of the input array.
+    */
     TECA_ALGORITHM_PROPERTY(std::string, component_variable)
 
-    // set this only if you know for certain that label ids are contiguous and
-    // start at 0. this enables use of a faster implementation.
+    /*! \fn set_contiguous_component_ids(const long &v)
+
+       set the label used for cells inside the segmentation.
+
+       \warning set this only if you know for certain that label ids are contiguous and
+                start at 0. this enables use of a faster implementation.
+    */
+    /*! \fn get_contiguous_component_ids() const
+
+       get the label used for cells inside the segmentation.
+    */
     TECA_ALGORITHM_PROPERTY(int, contiguous_component_ids)
 
-    // set this to override the component label used for background. By default
-    // this is set to -1 to indicate that the value should be obtained from the
-    // metadata key `background_id`.  Note that TECA's connected component
-    // labeler uses the id 0 for the background and passes this in a metadata
-    // key and as a result no action is required.
+    /*! \fn set_background_id(const long &v)
+
+       set the label used for cells outside of the segmentation,
+       i.e. the background. This can be used to skip processing
+       of the background when desirable.
+    */
+    /*! \fn get_background_id() const
+
+       get the label used for cells outside of the segmentation,
+       i.e. the background. This can be used to skip processing
+       of the background when desirable.
+    */
     TECA_ALGORITHM_PROPERTY(long, background_id)
 
 protected:

core/teca_algorithm_fwd.h

@@ -32,6 +32,7 @@ std::shared_ptr<T const> shared_from_this() const   \
 }
 
 #define TECA_ALGORITHM_CLASS_NAME(T)                \
+/*! returns the string value "T" */                 \
 const char *get_class_name() const override         \
 {                                                   \
     return #T;                                      \
@@ -50,6 +51,12 @@ const char *get_class_name() const override         \
 // convenience macro to declare standard set_X/get_X methods
 // where X is the name of a class member. will manage the
 // algorithm's modified state for the user.
+/*
+  \def TECA_ALGORITHM_PROPERTY(T, NAME)
+  convenience macro to declare standard set_X/get_X methods
+  where X is the name of a class member. will manage the
+  algorithm's modified state for the user.
+*/
 #define TECA_ALGORITHM_PROPERTY(T, NAME) \
                                          \
 void set_##NAME(const T &v)              \

doc/doxygen/Doxyfile

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "My Project"
+PROJECT_NAME           = "TECA"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -483,6 +483,7 @@ NUM_PROC_THREADS       = 1
 # The default value is: NO.
 
 EXTRACT_ALL            = NO
+#EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -844,8 +845,8 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-#INPUT                  = ../../alg/teca_bayesian_ar_detect.h
-INPUT                  = ../..
+INPUT                  = ../../alg/teca_2d_component_area.h
+#INPUT                  = ../..
 #INPUT                  =
 
 # This tag can be used to specify the character encoding of the source files
@@ -1128,7 +1129,7 @@ IGNORE_PREFIX          =
 # If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
 # The default value is: YES.
 
-GENERATE_HTML          = YES
+GENERATE_HTML          = NO
 
 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -2147,15 +2148,17 @@ SEARCH_INCLUDES        = YES
 # preprocessor.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
-INCLUDE_PATH           =
+#INCLUDE_PATH           =
+INCLUDE_PATH           = ../../core
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the
 # directories. If left blank, the patterns specified with FILE_PATTERNS will be
 # used.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-INCLUDE_FILE_PATTERNS  =
+#INCLUDE_FILE_PATTERNS  =
+INCLUDE_FILE_PATTERNS  = *.h
 
 # The PREDEFINED tag can be used to specify one or more macro names that are
 # defined before the preprocessor is started (similar to the -D option of e.g.
@@ -2185,6 +2188,7 @@ EXPAND_AS_DEFINED      =
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 SKIP_FUNCTION_MACROS   = YES
+#SKIP_FUNCTION_MACROS   = NO
 
 #---------------------------------------------------------------------------
 # Configuration options related to external references

doc/rtd/conf.py

@@ -30,7 +30,7 @@
 read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
 
 if read_the_docs_build:
-    subprocess.call('cd ../doxygen; doxygen', shell=True)
+    subprocess.call('cd ../doxygen; doxygen -d Preprocessor', shell=True)
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom

doc/rtd/framework/alg.rst

@@ -6,8 +6,6 @@ Classes
 
 .. doxygenclass:: teca_2d_component_area
    :members:
-   :protected-members:
-   :private-members:
    :undoc-members:
 
 .. doxygenclass:: teca_bayesian_ar_detect

doc/rtd/framework/framework.rst

@@ -2,11 +2,10 @@ Framework
 =========
 
 TECA provides an extensive suite of algorithms and software utilities
-to build Climage Data Analysis pipelines
-for climate data analysis.
+to build Climage Data Analysis/Transformation pipelines.
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contents:
 
    alg